Bone marrow transplantation is the treatment of choice for children with severe aplastic anemia who have a donor compatible in human leukocyte antigen system. The great problem of this therapy is the high rejection rate in patients who received the classic conditioning only with cyclophosphamide, mainly in the polytransfused patients, in the pre-transplant. Aiming to reduce the rejection rates, we chose the association of total body irradiation with 300 cGy to cyclophosphamide 50 mg/kg/day, intravenous, for four days in children younger than 12 years old, with severe aplastic anemia, from January 1991 to December 2001. Of the thirteen patients enrolled in this study the findings were: Disease-free survival rate of 92.3% in 120 months; global survival rate of 84.6% in 140 months; the immediate toxicity related to the treatment was minimal and impaired growth of four children. However, these children were already enrolled in our study with deficiency in their height, and it is difficult to prove a correlation with the conditioning regimen. There were reductions of the insulin-like growth factors hormone serious level, normalization of the growth hormone and binding of protein-3 in most of the cases studied. The assessment of the thyroid hormones was also carried out and alterations concerning the serious level were not observed. An ophthalmologic assessment was carried out and cataracts was not observed and the assessment concerning the sexual development showed normality of the secondary sexual characteristics and normal hormonal levels as well. There was no rejection in the patients evaluated.